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. 2020 Oct 9;48(19):e114. doi: 10.1093/nar/gkaa829

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© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 6. — Illustration of how unreliable PSVs adversely impact short-read variant calling in segmental duplications. An Integrated Genomics Viewer view of a duplicated region on chromosome 7 that overlaps the PMS2 gene is shown. A PSV is located at chr7:5972749 (allele = with the homologous position at chr7:6752042). Variant calling on PacBio CCS reads (aligned with DuploMap) identifies two variants, a homozygous variant at the PSV site (chr7:5972749:CA:TG) and a heterozygous SNV located nearby (chr7:5972674:C:G). Both of these variants are supported by 10X Genomics variant calls but are absent from short-read variant calls for the same individual (PG VCF track). In addition, short-read variant calling results in a false SNV (chr7:6752118:G:C) at the position homologous to chr7:5972674—a result of short-read mismapping due to the unreliable PSV.